Column sorting: rapid calculation of the phylogenetic likelihood function.

@article{Pond2004ColumnSR,
  title={Column sorting: rapid calculation of the phylogenetic likelihood function.},
  author={Sergei L. Kosakovsky Pond and Spencer V. Muse},
  journal={Systematic biology},
  year={2004},
  volume={53 5},
  pages={685-92}
}
Likelihood applications have become a central approach for molecular evolutionary analyses since the first computationally tractable treatment two decades ago. Although Felsenstein's original pruning algorithm makes likelihood calculations feasible, it is usually possible to take advantage of repetitive structure present in the data to arrive at even greater computational reductions. In particular, alignment columns with certain similarities have components of the likelihood calculation that… CONTINUE READING
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